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My profesional experience is in systems administration, cloud architecture, and automation, with considerations for corporate disaster recovery and regular 3rd party audits.
The short answer to all of your questions boil down to two things;
1: If you're going to maintain a system, write a script to build it, then use the script (I'll expand this below).
2: Expect a catastrophic failure. Total loss, server gone. As such; backup all unique or user-generated data regularly, and practice restoring it.
Okay back to #1; I prefer shell scripts (pick your favorite shell, doesn't matter which), because there are basically zero requirements. Your system will have your preferred shell installed within minutes of existing, there is no possibility that it won't. But why shell? Because then you don't need docker, or python, or a specific version of a specifc module/plugin/library/etc.
So okay, we're gonna write a script. "I should install by hand as I'm taking down notes" right? Hell, "I can write the script as I'm manually installing", "why can't that be my notes?". All totally valid, I do that too. But don't use the manually installed one and call it done. Set the server on fire, make a new one, run the script. If everything works, you didn't forget that "oh right, this thing real quick" requirement. You know your script will bring you from blank OS to working server.
Once you have those, the worst case scenario is "shit, it's gone... build new server, run script, restore backup". The penalty for critical loss of infrastructure is some downtime. If you want to avoid that, see if you can install the app on two servers, the DB on another two (with replication), and set up a cluster. Worst case (say the whole region is deleted) is the same; make new server, run script, restore backups.
If you really want to get into docker or etc after that, there's no blocker. You know how the build the system "bare metal", all that's left is describing it to docker. Or cloudformation, terraform, etc, etc, etc. I highly recommend doing it with shell first, because A: You learn a lot about the system and B: you're ready to troubleshoot it (if you want to figure out why it failed and try to mitigate it before it happens again, rather than just hitting "reset" every time).
I just started my mbin instance a week or two ago. When I did, I wrote a guided install script (it's a long story, but I ended up having to blow away the server like 7 times and re-install).
This might be overkill for your purposes, but it's the kind of thing I have in mind.
Note1: Sorry, it's kinda sloppy. I need to clean it up before I submit a PR to the mbin devs for possible inclusion in their documentation. Note2: It assumes that you're running a single-user instance, and on a single, small server, with no external requirements.
https://alexanderesmith.com/mbin/install_mbin.bash